Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  HUMAN SCAVENGER RECEPTOR C-TYPE LECTIN CARBOHYDRATE-RECOGNITION DOMAIN.
 
Authors :  W. I. Weis, H. Feinberg, K. Drickamer, M. E. Taylor
Date :  20 Feb 07  (Deposition) - 03 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  C-Type Lectin, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Feinberg, M. E. Taylor, W. I. Weis
Scavenger Receptor C-Type Lectin Binds To The Leukocyte Cell Surface Glycan Lewis(X) By A Novel Mechanism.
J. Biol. Chem. V. 282 17250 2007
PubMed-ID: 17420244  |  Reference-DOI: 10.1074/JBC.M701624200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SCAVENGER RECEPTOR WITH C-TYPE LECTIN TYPE I
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCRD DOMAIN
    GeneSRCL
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 34)

Asymmetric Unit (3, 34)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2CL12Ligand/IonCHLORIDE ION
3ZN16Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (34, 34)

Asymmetric Unit (34, 34)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECL A:6 , CL A:7 , HIS A:610 , HIS A:641BINDING SITE FOR RESIDUE ZN A 1
02AC2SOFTWARECL A:8 , TYR A:619 , PHE A:644 , GLU A:650 , GLU A:731BINDING SITE FOR RESIDUE ZN A 2
03AC3SOFTWAREASP A:616 , LYS A:617 , ASP A:733 , HOH A:743 , HIS B:700BINDING SITE FOR RESIDUE ZN A 3
04AC4SOFTWAREASP A:670 , GLU A:674 , HIS A:702 , ASP A:707BINDING SITE FOR RESIDUE ZN A 4
05AC5SOFTWAREGLU A:662 , HIS A:664 , HOH A:744 , HOH A:746BINDING SITE FOR RESIDUE ZN A 5
06AC6SOFTWAREZN A:1 , HIS A:610 , HIS A:641 , ASP A:733BINDING SITE FOR RESIDUE CL A 6
07AC7SOFTWAREZN A:1 , HIS A:610 , LYS A:617 , GLU A:731BINDING SITE FOR RESIDUE CL A 7
08AC8SOFTWAREZN A:2 , PHE A:644 , ASN A:646 , GLU A:650 , GLU A:731BINDING SITE FOR RESIDUE CL A 8
09AC9SOFTWARECL B:6 , CL B:7 , HIS B:610 , HIS B:641BINDING SITE FOR RESIDUE ZN B 1
10BC1SOFTWARECL B:8 , PHE B:644 , GLU B:650 , GLU B:731BINDING SITE FOR RESIDUE ZN B 2
11BC2SOFTWAREHIS A:700 , HOH A:745 , ASP B:616 , ASP B:733BINDING SITE FOR RESIDUE ZN B 3
12BC3SOFTWAREASP B:670 , GLU B:674 , HIS B:702 , ASP B:707BINDING SITE FOR RESIDUE ZN B 4
13BC4SOFTWAREGLU B:662 , HIS B:664 , HOH B:743BINDING SITE FOR RESIDUE ZN B 5
14BC5SOFTWAREZN B:1 , HIS B:610 , HIS B:641 , ASP B:733BINDING SITE FOR RESIDUE CL B 6
15BC6SOFTWAREZN B:1 , HIS B:610 , LYS B:617 , HIS B:641 , GLU B:731BINDING SITE FOR RESIDUE CL B 7
16BC7SOFTWAREZN B:2 , PHE B:644 , GLU B:650 , GLU B:731BINDING SITE FOR RESIDUE CL B 8
17BC8SOFTWARECL C:3 , CL C:4 , HIS C:610 , HIS C:641 , TRP D:611 , LYS D:612 , TYR D:619 , TYR D:620BINDING SITE FOR RESIDUE ZN C 1
18BC9SOFTWARECL C:5 , PHE C:644 , GLU C:650 , GLU C:731 , PHE D:621 , SER D:622BINDING SITE FOR RESIDUE ZN C 2
19CC1SOFTWAREZN C:1 , HIS C:641 , LYS C:732 , ASP C:733 , TRP D:611 , LYS D:612 , CYS D:618 , TYR D:619BINDING SITE FOR RESIDUE CL C 3
20CC2SOFTWAREZN C:1 , HIS C:610 , HIS C:641 , GLU C:731 , TYR D:619 , TYR D:620 , PHE D:621BINDING SITE FOR RESIDUE CL C 4
21CC3SOFTWAREZN C:2 , LYS C:617 , PHE C:644 , GLU C:650 , GLU C:731 , TYR D:620 , PHE D:621 , SER D:622BINDING SITE FOR RESIDUE CL C 5
22CC4SOFTWAREASP C:670 , GLU C:674 , ASN C:697 , GLU C:706 , ASP C:707BINDING SITE FOR RESIDUE CA C 6
23CC5SOFTWAREGLN C:694 , ASP C:696 , GLU C:706 , ASN C:718 , ASP C:719BINDING SITE FOR RESIDUE CA C 7
24CC6SOFTWAREGLU C:674 , PRO C:704 , ASP C:707BINDING SITE FOR RESIDUE CA C 8
25CC7SOFTWAREASP B:696 , HOH C:32 , HIS C:700BINDING SITE FOR RESIDUE ZN C 9
26CC8SOFTWARETRP C:611 , LYS C:612 , TYR C:619 , TYR C:620 , CL D:3 , CL D:4 , HIS D:610 , HIS D:641BINDING SITE FOR RESIDUE ZN D 1
27CC9SOFTWAREPHE C:621 , SER C:622 , CL D:5 , PHE D:644 , GLU D:650 , GLU D:731BINDING SITE FOR RESIDUE ZN D 2
28DC1SOFTWARETRP C:611 , LYS C:612 , CYS C:618 , TYR C:619 , ZN D:1 , HIS D:641BINDING SITE FOR RESIDUE CL D 3
29DC2SOFTWAREHIS C:610 , TRP C:611 , LYS C:612 , TYR C:619 , TYR C:620 , PHE C:621 , ZN D:1 , HIS D:610 , LYS D:617 , HIS D:641 , GLU D:731BINDING SITE FOR RESIDUE CL D 4
30DC3SOFTWARETYR C:620 , PHE C:621 , SER C:622 , ZN D:2 , PHE D:644 , GLU D:650 , GLU D:731BINDING SITE FOR RESIDUE CL D 5
31DC4SOFTWAREASP D:670 , GLU D:674 , ASN D:697 , GLU D:706 , ASP D:707BINDING SITE FOR RESIDUE CA D 6
32DC5SOFTWAREGLN D:694 , ASP D:696 , GLU D:706 , ASN D:718 , ASP D:719BINDING SITE FOR RESIDUE CA D 7
33DC6SOFTWAREGLU D:674 , ASP D:707BINDING SITE FOR RESIDUE CA D 8
34DC7SOFTWAREASP A:696 , HOH D:33 , HIS D:700BINDING SITE FOR RESIDUE ZN D 9

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:607 -A:618
2A:635 -A:730
3A:708 -A:722
4B:607 -B:618
5B:635 -B:730
6B:708 -B:722
7C:607 -C:618
8C:635 -C:730
9C:708 -C:722
10D:607 -D:618
11D:635 -D:730
12D:708 -D:722

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gln A:694 -Pro A:695
2Gln B:694 -Pro B:695
3Gln C:694 -Pro C:695
4Gln D:694 -Pro D:695

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 4)

Asymmetric Unit (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_038856G606SCOL12_HUMANPolymorphism2305027A/B/C/DS606S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_038856G606SCOL12_HUMANPolymorphism2305027AS606S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_038856G606SCOL12_HUMANPolymorphism2305027BS606S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_038856G606SCOL12_HUMANPolymorphism2305027CS606S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 4 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_038856G606SCOL12_HUMANPolymorphism2305027DS606S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.COL12_HUMAN614-731
 
 
 
  4A:614-731
B:614-731
C:614-731
D:614-731
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.COL12_HUMAN708-730
 
 
 
  4A:708-730
B:708-730
C:708-730
D:708-730
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.COL12_HUMAN614-731
 
 
 
  1A:614-731
-
-
-
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.COL12_HUMAN708-730
 
 
 
  1A:708-730
-
-
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.COL12_HUMAN614-731
 
 
 
  1-
B:614-731
-
-
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.COL12_HUMAN708-730
 
 
 
  1-
B:708-730
-
-
Biological Unit 3 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.COL12_HUMAN614-731
 
 
 
  1-
-
C:614-731
-
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.COL12_HUMAN708-730
 
 
 
  1-
-
C:708-730
-
Biological Unit 4 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.COL12_HUMAN614-731
 
 
 
  1-
-
-
D:614-731
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.COL12_HUMAN708-730
 
 
 
  1-
-
-
D:708-730

(-) Exons   (4, 16)

Asymmetric Unit (4, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000004002561ENSE00001542175chr18:500729-500508222COL12_HUMAN1-330--
1.2ENST000004002562ENSE00001240662chr18:480757-48070751COL12_HUMAN3-20180--
1.3ENST000004002563ENSE00000901812chr18:357522-357400123COL12_HUMAN20-61420--
1.4ENST000004002564ENSE00001038050chr18:348163-34806599COL12_HUMAN61-94340--
1.5ENST000004002565ENSE00001038056chr18:347341-3462951047COL12_HUMAN94-4433500--
1.6ENST000004002566ENSE00001208502chr18:335230-334742489COL12_HUMAN443-6061644A:606-606
B:606-606
C:606-606
D:606-606
1
1
1
1
1.7ENST000004002567ENSE00001240712chr18:333143-333007137COL12_HUMAN606-651464A:606-651
B:606-651
C:606-651
D:606-651
46
46
46
46
1.8ENST000004002568ENSE00001148017chr18:331777-331668110COL12_HUMAN652-688374A:652-688
B:652-688
C:652-688
D:652-688
37
37
37
37
1.9ENST000004002569ENSE00001208518chr18:321807-321662146COL12_HUMAN688-737504A:688-734
B:688-734
C:688-734
D:688-734
47
47
47
47
1.10ENST0000040025610ENSE00001386587chr18:320064-319355710COL12_HUMAN737-74260--

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:129
 aligned with COL12_HUMAN | Q5KU26 from UniProtKB/Swiss-Prot  Length:742

    Alignment length:129
                                   615       625       635       645       655       665       675       685       695       705       715       725         
          COL12_HUMAN   606 GCPPHWKNFTDKCYYFSVEKEIFEDAKLFCEDKSSHLVFINTREEQQWIKKQMVGRESHWIGLTDSERENEWKWLDGTSPDYKNWKAGQPDNWGHGHGPGEDCAGLIYAGQWNDFQCEDVNNFICEKDR 734
               SCOP domains d2ox8a_ A: automated matches                                                                                                      SCOP domains
               CATH domains 2ox8A00 A:606-734 Mannose-Binding Protein A, subunit A                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhh.....eeeeee........ee............................eeee.....eeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) S-------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: A:614-731 UniProt: 614-731                                                                      --- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1        ---- PROSITE (2)
           Transcript 1 (1) 1---------------------------------------------Exon 1.8  PDB: A:652-688             ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.7  PDB: A:606-651 UniProt: 606-651     ------------------------------------Exon 1.9  PDB: A:688-734 UniProt: 688-737       Transcript 1 (2)
                 2ox8 A 606 SCPPHWKNFTDKCYYFSVEKEIFEDAKLFCEDKSSHLVFINTREEQQWIKKQMVGRESHWIGLTDSERENEWKWLDGTSPDYKNWKAGQPDNWGHGHGPGEDCAGLIYAGQWNDFQCEDVNNFICEKDR 734
                                   615       625       635       645       655       665       675       685       695       705       715       725         

Chain B from PDB  Type:PROTEIN  Length:129
 aligned with COL12_HUMAN | Q5KU26 from UniProtKB/Swiss-Prot  Length:742

    Alignment length:129
                                   615       625       635       645       655       665       675       685       695       705       715       725         
          COL12_HUMAN   606 GCPPHWKNFTDKCYYFSVEKEIFEDAKLFCEDKSSHLVFINTREEQQWIKKQMVGRESHWIGLTDSERENEWKWLDGTSPDYKNWKAGQPDNWGHGHGPGEDCAGLIYAGQWNDFQCEDVNNFICEKDR 734
               SCOP domains d2ox8b_ B: automated matches                                                                                                      SCOP domains
               CATH domains 2ox8B00 B:606-734 Mannose-Binding Protein A, subunit A                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeee....eehhhhhhhhhh...ee....hhhhhhhhhhh......eeeeee........ee............................eeee.....eeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) S-------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: B:614-731 UniProt: 614-731                                                                      --- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1        ---- PROSITE (2)
           Transcript 1 (1) 1---------------------------------------------Exon 1.8  PDB: B:652-688             ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.7  PDB: B:606-651 UniProt: 606-651     ------------------------------------Exon 1.9  PDB: B:688-734 UniProt: 688-737       Transcript 1 (2)
                 2ox8 B 606 SCPPHWKNFTDKCYYFSVEKEIFEDAKLFCEDKSSHLVFINTREEQQWIKKQMVGRESHWIGLTDSERENEWKWLDGTSPDYKNWKAGQPDNWGHGHGPGEDCAGLIYAGQWNDFQCEDVNNFICEKDR 734
                                   615       625       635       645       655       665       675       685       695       705       715       725         

Chain C from PDB  Type:PROTEIN  Length:129
 aligned with COL12_HUMAN | Q5KU26 from UniProtKB/Swiss-Prot  Length:742

    Alignment length:129
                                   615       625       635       645       655       665       675       685       695       705       715       725         
          COL12_HUMAN   606 GCPPHWKNFTDKCYYFSVEKEIFEDAKLFCEDKSSHLVFINTREEQQWIKKQMVGRESHWIGLTDSERENEWKWLDGTSPDYKNWKAGQPDNWGHGHGPGEDCAGLIYAGQWNDFQCEDVNNFICEKDR 734
               SCOP domains d2ox8c_ C: automated matches                                                                                                      SCOP domains
               CATH domains 2ox8C00 C:606-734 Mannose-Binding Protein A, subunit A                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhh......eeeeee........ee............................eeee.....eeee........eeeee. Sec.struct. author
                 SAPs(SNPs) S-------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: C:614-731 UniProt: 614-731                                                                      --- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1        ---- PROSITE (2)
           Transcript 1 (1) 1---------------------------------------------Exon 1.8  PDB: C:652-688             ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.7  PDB: C:606-651 UniProt: 606-651     ------------------------------------Exon 1.9  PDB: C:688-734 UniProt: 688-737       Transcript 1 (2)
                 2ox8 C 606 SCPPHWKNFTDKCYYFSVEKEIFEDAKLFCEDKSSHLVFINTREEQQWIKKQMVGRESHWIGLTDSERENEWKWLDGTSPDYKNWKAGQPDNWGHGHGPGEDCAGLIYAGQWNDFQCEDVNNFICEKDR 734
                                   615       625       635       645       655       665       675       685       695       705       715       725         

Chain D from PDB  Type:PROTEIN  Length:129
 aligned with COL12_HUMAN | Q5KU26 from UniProtKB/Swiss-Prot  Length:742

    Alignment length:129
                                   615       625       635       645       655       665       675       685       695       705       715       725         
          COL12_HUMAN   606 GCPPHWKNFTDKCYYFSVEKEIFEDAKLFCEDKSSHLVFINTREEQQWIKKQMVGRESHWIGLTDSERENEWKWLDGTSPDYKNWKAGQPDNWGHGHGPGEDCAGLIYAGQWNDFQCEDVNNFICEKDR 734
               SCOP domains d2ox8d_ D: automated matches                                                                                                      SCOP domains
               CATH domains 2ox8D00 D:606-734 Mannose-Binding Protein A, subunit A                                                                            CATH domains
           Pfam domains (1) ------------------Lectin_C-2ox8D01 D:624-732                                                                                   -- Pfam domains (1)
           Pfam domains (2) ------------------Lectin_C-2ox8D02 D:624-732                                                                                   -- Pfam domains (2)
           Pfam domains (3) ------------------Lectin_C-2ox8D03 D:624-732                                                                                   -- Pfam domains (3)
           Pfam domains (4) ------------------Lectin_C-2ox8D04 D:624-732                                                                                   -- Pfam domains (4)
         Sec.struct. author ......eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhh.......eeeeee........ee............................eeee.....eeee........eeeee. Sec.struct. author
                 SAPs(SNPs) S-------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: D:614-731 UniProt: 614-731                                                                      --- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1        ---- PROSITE (2)
           Transcript 1 (1) 1---------------------------------------------Exon 1.8  PDB: D:652-688             ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.7  PDB: D:606-651 UniProt: 606-651     ------------------------------------Exon 1.9  PDB: D:688-734 UniProt: 688-737       Transcript 1 (2)
                 2ox8 D 606 SCPPHWKNFTDKCYYFSVEKEIFEDAKLFCEDKSSHLVFINTREEQQWIKKQMVGRESHWIGLTDSERENEWKWLDGTSPDYKNWKAGQPDNWGHGHGPGEDCAGLIYAGQWNDFQCEDVNNFICEKDR 734
                                   615       625       635       645       655       665       675       685       695       705       715       725         

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: C_Lectin (98)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (COL12_HUMAN | Q5KU26)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0005534    galactose binding    Interacting selectively and non-covalently with the aldohexose galactose (galacto-hexose), a common constituent of many oligo- and polysaccharides.
    GO:0030169    low-density lipoprotein particle binding    Interacting selectively and non-covalently with a low-density lipoprotein particle, a lipoprotein particle that is rich in cholesterol esters and low in triglycerides, is typically composed of APOB100 and APOE, and has a density of 1.02-1.06 g/ml and a diameter of between 20-25 nm.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005044    scavenger receptor activity    Combining with any modified low-density lipoprotein (LDL) or other polyanionic ligand and delivering the ligand into the cell via endocytosis. Ligands include acetylated and oxidized LDL, Gram-positive and Gram-negative bacteria, apoptotic cells, amyloid-beta fibrils, and advanced glycation end products (AGEs).
    GO:0008329    signaling pattern recognition receptor activity    Combining with a pathogen-associated molecular pattern (PAMP), a structure conserved among microbial species, or damage-associated molecular pattern (DAMP), an endogenous molecule released from damaged cells), and transmitting a signal to initiate a change in cell activity.
biological process
    GO:0009756    carbohydrate mediated signaling    A series of molecular signals mediated by the detection of carbohydrate.
    GO:0071360    cellular response to exogenous dsRNA    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an exogenous double-stranded RNA stimulus.
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0006910    phagocytosis, recognition    The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
    GO:0060355    positive regulation of cell adhesion molecule production    Any process that increases the rate, frequency or extent of cell adhesion molecule production. Cell adhesion molecule production is the appearance of a cell adhesion molecule as a result of its biosynthesis or a decrease in its catabolism.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    GO:0034138    toll-like receptor 3 signaling pathway    Any series of molecular signals generated as a consequence of binding to toll-like receptor 3.
cellular component
    GO:0005581    collagen trimer    A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
    GO:0030666    endocytic vesicle membrane    The lipid bilayer surrounding an endocytic vesicle.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
    CC7  [ RasMol ]  +environment [ RasMol ]
    CC8  [ RasMol ]  +environment [ RasMol ]
    CC9  [ RasMol ]  +environment [ RasMol ]
    DC1  [ RasMol ]  +environment [ RasMol ]
    DC2  [ RasMol ]  +environment [ RasMol ]
    DC3  [ RasMol ]  +environment [ RasMol ]
    DC4  [ RasMol ]  +environment [ RasMol ]
    DC5  [ RasMol ]  +environment [ RasMol ]
    DC6  [ RasMol ]  +environment [ RasMol ]
    DC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln A:694 - Pro A:695   [ RasMol ]  
    Gln B:694 - Pro B:695   [ RasMol ]  
    Gln C:694 - Pro C:695   [ RasMol ]  
    Gln D:694 - Pro D:695   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2ox8
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  COL12_HUMAN | Q5KU26
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  COL12_HUMAN | Q5KU26
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 2OX8)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2OX8)